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Thursday, March 30, 2017

You cannot have missed it, and if you did, you know about it know. We're marching for science. Originating in the USA, the marches are spreading around the world, also in Europe. More than 400 was the count a week ago. One by one, European cities joined with initiatives. Science March Stockholm was the first to get my interest, but Science March Amsterdam followed soon after. So, no reason to return to Stockholm this April. Here's a map with all planned marches around the world:

Zooming in on Europe (well, part of it), we get this map:

Quite a bit of choice. We see several countries with multiple marches. The Netherlands shows the Amsterdam march, but ideas have been posed to organize a Science March in Maastricht too.

Well, I will be marching. For what? For the importance of apolitical, nonreligious facts about the world. Facts that can be proven true, but also for a world where people value facts, fulfilling the human rights for everyone, as facts don't care about race, gender, color, left, right, or nerdiness.

Our world is precious; human and nature is precious. If we choose to destroy the world or if we choose to prosper mankind and nature, let it because of neutral facts. Not wishful thinking, money, or politics.

Let's show that science (of any domain, not just life sciences, but also humanities, etc) is by everyone and for everyone. Access to knowledge is a human right, is to benefit everyone. The march is for everyone too: you do not have to be working in scientific research to join the march to express your wish to have a fact-based country.

Tuesday, March 21, 2017

Already many months ago I joined a bio.tools (doi:10.1093/nar/gkv1116) workshop in Amsterdam, organized by Gert Vriendet al (see this coverage). I learned then how to register services, search, and that underneath JSON is used in the API to exchange information about the services. One neat feature is that bio.tools allows you to specify a lot of detail of the service calls.

Now, at the time we had already used OpenAPI (then still called Swagger) for Open PHACTS for some time, which we later picked up for other projects, like eNanoMapper (API), WikiPathways (API), and BridgeDb (API). OpenAPI configuration files also describe how web services work. So, the idea arose to that it should be possible to convert the first to the second. Simple. I started a GitHub repository, but, of course, did not really have time to implement it.

Then, half a year ago, at the ELIXIR track meeting at the ECCB in The Hague (where I presented this BridgeDb poster), I spoke with people from ELIXIR-DK who were just starting a studentship scheme. This led to a project idea, then a proposal, and then an small, approved project, allowing me to fund Jonathan Mélius to work on this part-time, for about a man month of work, spread over several months.

Jonathan has been doing great work, and because we liked to demo the OpenAPI 2 bio.tools bridge with a major European resource, Ensembl was suggested (which just published a paper on their core software). An OpenAPI for Ensembl was set up, which is going to be the primary input for the new tool:

The observant eye will see that various bits of details of the descriptions of the API calls are annotated with EDAM ontology (doi:10.1093/bioinformatics/btt113) terms, a key feature of bio.tools. This information is currently not available in the OpenAPI JSON (we will be exploring how that specification could/should be extended to do this). Moreover, the webservice API methods need ontological annotation in the first place, and we will not be able to totally remove human involvement there.

The EDAM IRIs are still hard-coded in the conversion tool at this moment, but are being factored out into a secondary JSON file for now. So, the conversion tool will take two input JSON files, OpenAPI + EDAM annotation, and create bio.tools JSON output. The latter can then be inserted into the JSON. We will work on something based on the bio.tools API to automate that step too.

So, we still have some work to do, but I'm happy with the current progress. We're well on track to complete this project before summer and actually get a long way with the ontology annotation, which was an secondary in the original plan.

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised and atomic level. Open Science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and WikiPathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.

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